Association of SRAP markers with juvenile wood basic density and growth traits in Cunninghamia lanceolata (Lamb.) Hook

• Języki publikacji: EN

Abstrakty

EN

Application of sequence-related amplified polymorphism (SRAP) markers to unravel variations and relationships with biological and morphological traits has been reported in a variety of plant species, and their potential for breeding has also been highlighted. (1) Assess the diversity level of a Cunninghamia lanceolata (Chinese fir) genetic panel based on phenotypic traits and SRAP markers, (2) identify SRAP loci linked to juvenile wood basic density (JWBD) and growth traits, and (3) address the overlap of the trait-associated SRAP markers during the juvenile and mature stages of this species. A total of 227 Chinese fir genotypes were subjected to phenotype, SRAP genotyping, and marker-trait association analyses. A total of 564 unambiguous SRAP bands and 558 polymorphic loci were identified from the genotypes. The overall percentage of polymorphic bands, polymorphism information content, Nei’s gene diversity, and Shannon’s Information Index were 98.9%, 0.2576, 0.3196 and 0.4838, respectively. An analysis of molecular variance further demonstrated that the genotypes varied significantly at SRAP polymorphisms (p < 0.01). A wide genetic distance span from 0.0531 to 0.9097 was also observed; most (94.9%) fell within the range of 0.3000–0.6999. An association analysis based on general linear model (GLM) and mixed linear model (MLM) unraveled 21, 26, 25, and 19 marker-trait associations for JWBD, height (H), diameter at breast height (DBH, 1.3 m) and stem volume (V), respectively. These marker-trait associations corresponded to 64 different SRAP markers; 46 of these were linked to only one trait, while the other 18 markers appeared to be associated with more than one trait but limited to growth traits. Overall, the SRAP markers represented R2 (percentage of the phenotypic variation explained by marker) values of 1.7–9.2% for the GLM and 1.7–5.6% for the MLM. Strikingly, the significant trait-associated marker list seemed to be rather different from that of the previous study performed on mature traits (WBD, H, DBH and V), except for overlap of two markers. This study demonstrated an association of SRAP markers with JWBD and growth traits in Chinese fir. The results further our understanding of the genetic basis of the Chinese fir WBD and growth traits at the juvenile stage.

• Wydawca: -
• Czasopismo: Dendrobiology
• Rocznik: 2018
• Tom: 79
• Opis fizyczny: p.111–118,fig.,ref.

Twórcy

Bibliografia

• Achar D, Awati MG, Udayakumar M & Prasad TG (2015) Identification of putative molecular markers associated with root traits in Coffea canephora Pierre ex Froehner. Molecular Biology International 2015: 532386. doi:10.1155/2015/532386.
• Agarwal M, Shrivastava N & Padh H (2008) Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Reports 27: 617–631. doi:10.1007/s00299-008-0507-z.
• Aneja B, Yadav NR, Chawla V & Yadav RC (2012) Sequence-related amplified polymorphism (SRAP) molecular marker system and its applications in crop improvement. Molecular Breeding 30: 1635–1648. doi:10.1007/s11032-012-9747-2.
• Beaulieu J, Doerksen T, Boyle B, Clément S, Deslauriers M, Beauseigle S, Blais S, Poulin PL, Lenz P, Caron S, Rigault P, Bicho P, Bousquet J & Mackay J (2011) Association genetics of wood physical traits in the conifer white spruce and relationships with gene expression. Genetics 188: 197–214. doi:10.1534/genetics.110.125781.
• Boruszewski P, Jankowska A & Kurowska A (2017) Comparison of the structure of juvenile and mature wood of Larix decidua Mill. from fast-growing plantations in Poland. Bioresources 12 : 1813–1825.
• Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y & Buckler ES (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23: 2633–2635. doi:10.1093/bioinformatics/btm308.
• Dadras AR, Sabouri H, Nejad GM, Sabouri A & Shoai-Deylami M (2014) Association analysis, genetic diversity and structure analysis of tobacco based on AFLP markers. Molecular Biology Reports 41: 3317–3329. doi:10.1007/s11033-014-3194-6.
• Duan HJ, Hu DH, Li Y & Zheng HQ (2016) Characterization of a collection of Chinese fir elite gen otypes using sequence-related amplified polymorphism markers. Journal of Forestry Research 27: 1105–1110. doi:10.1007/s11676-016-0233-2.
• Eckert AJ, Bower AD, Wegrzyn JL, Pande B, Jermstad KD, Krutovsky KV, St Clair JB & Neale DB (2009) Association genetics of coastal Douglas fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-hardiness related traits. Genetics 182: 1289–302. doi:10.1534/genetics.109.102350.
• Eckert AJ, Wegrzyn JL, Cumbie WP, Goldfarb B, Huber DA, Tolstikov V, Fiehn O & Neale DB (2012) Association genetics of the loblolly pine (Pinus taeda, Pinaceae) metabolome. New Phytologist 193: 890–902. doi:10.1111/j.1469-8137.2011.03976.x.
• Ganopoulos I, Merkouropoulos G, Pantazis S, Tsipouridis C & Tsaftaris A (2011) Assessing molecular and morpho-agronomical diversity and identification of ISSR markers associated with fruit traits in quince (Cydonia oblonga). Genetics and Molecular Research 10: 2729–2746. doi:10.4238/2011.November.4.7.
• Ganthaler A, Stöggl W, Mayr S, Kranner I, Schüler S, Wischnitzki E, Sehr EM, Fluch S & Trujillo-Moya C (2017) Association genetics of phenolic needle compounds in Norway spruce with variable susceptibility to needle bladder rust. Plant Molecular Biology 94: 229–251. doi:10.1007/s11103-017-0589-5.
• González-Martínez SC, Wheeler NC, Ersoz E, Nelson CD & Neale DB (2007) Association genetics in Pinus taeda L. I. Wood property traits. Genetics 175: 399–409. doi:10.1534/genetics.106.061127.
• Khadivi-Khub A, Karimi E & Hadian J (2014) Population genetic structure and trait associations in forest savory using molecular, morphological and phytochemical markers. Gene 546: 297–308. doi:10.1016/j.gene.2014.05.062.
• Lamara M, Raherison E, Lenz P, Beaulieu J, Bousquet J & MacKay J (2016) Genetic architecture of wood properties based on association analysis and co-expression networks in white spruce. New Phytologist 210: 240–255. doi:10.1111/nph.13762.
• Lees CJ, Li G & Duncan RW (2016) Characterization of Brassica napus L. genotypes utilizing sequence-related amplified polymorphism and genotyping by sequencing in association with cluster analysis. Molecular Breeding 36: 155. doi:10.1007/s11 032-016-0576-6.
• Li G & Quiros CF (2001) Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theoretical and Applied Genetics 103: 455–461.
• Li M, Chen XZ, Huang MS, Wu PF & Ma XQ (2017) Genetic diversity and relationships of ancient Chinese fir (Cunninghamia lanceolata) genotypes revealed by sequence-related amplified polymorphism markers. Genetic Resources and Crop Evolution 64: 1087–1099. doi:10.1007/s10722-016-0428-6.
• Li X, Wu HX & Southerton SG (2012) Identification of putative candidate genes for juvenile wood density in Pinus radiata. Tree Physiology 32: 1046–1057. doi:10.1093/treephys/tps060.
• Liu K & Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128–2129. doi:10.1093/bioinformatics/bti282.
• Parchman TL, Gompert Z, Mudge J, Schilkey FD, Benkman CW & Buerkle CA (2012) Genome-wide association genetics of an adaptive trait in lodgepole pine. Molecular Ecology 21: 2991–3005. doi:10.1111/j.1365-294X.2012.05513.x.
• Pawar KD, Joshi SP & Thengane SR (2011) Association between chemical and genetic variation in Calophyllum inophyllum, a medicinally important tree of the Western Ghats of India. Plant Systematics and Evolution 292: 257–265. doi:10.1007/s00606-010-0409-8.
• Peakall R & Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28: 2537–2539. doi:10.1093/bioinformatics/bts460.
• Pereira da Costa JH, Rodríguez GR, Pratta GR, Picardi LA & Zorzoli R (2014) Pericarp polypeptides and SRAP markers associated with fruit quality traits in an interspecific tomato backcross. Genetics and Molecular Research 13: 2539–2547. doi:10.4238/2014.January.24.10.
• Prunier J, Pelgas B, Gagnon F, Desponts M, Isabel N, Beaulieu J & Bousquet J (2013) The genomic architecture and association genetics of adaptive characters using a candidate SNP approach in boreal black spruce. BMC Genomics 14: 368. doi:10.1186/1471-2164-14-368.
• Robarts DWH & Wolfe AD (2014) Sequence-related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology. Applications in Plant Sciences 2: 1400017. doi:10.3732/apps.1400017.
• Rohlf FJ (2000) NTSYSpc, numerical taxonomy and multivariate analysis system version 2.10e. Exeter Software, Setauket.
• Su Y, Hu DH & Zheng HQ (2016) Detection of SNPs based on DNA specific-locus amplified fragment sequencing in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook). Dendrobiology 76: 73–79. doi:10.12657/denbio.076.007.
• Uchiyama K, Iwata H, Moriguchi Y, Ujino-Ihara T, Ueno S, Taguchi Y, Tsubomura M, Mishima K, Iki T, Watanabe A, Futamura N, Shinohara K & Tsumura Y (2013) Demonstration of genome-wide association studies for identifying markers for wood property and male strobili traits in Cryptomeria japonica. PLoS One 8: e79866. doi:10.1371/journal.pone.0079866.
• Wang XQ, Yu Y, Li W, Guo HL, Lin ZX & Zhang XL (2013) Association analysis of yield and fiber quality traits in Gossypium barbadense with SSRs and SRAPs. Genetics and Molecular Research 12: 3353–3362. doi:10.4238/2013.September.4.1.
• Yeh FC, Yang RC & Boyle T (1999) PopGene: Microsoft Window-based freeware for population genetic analysis, version 1.31. University of Alberta and Center for International Forestry Research, Edmonton.
• Zhang YX, Han XJ, Sang J, He XL, Liu MY, Qiao GR, Zhuo RY, He GP & Hu JJ (2016) Transcriptome analysis of immature xylem in the Chinese fir at different developmental phases. Peer Journal 4: e2097. doi:10.7717/peerj.2097.
• Zheng HQ, Hu DH, Wei RP, Wang RH & Cai WJ (2012) Fast-growing clone selection and wood quality analysis in Chinese fir. Chinese Agricultural Science Bulletin 28: 27–31.
• Zheng HQ, Duan HJ, Hu DH, Wei RP & Li Y (2015a) Sequence-related amplified polymorphism primer screening on Chinese fir (Cunninghamia lanceolata (Lamb.) Hook). Journal of Forestry Research 26: 101–106. doi:10.1007/s11676-015-0025-0.
• Zheng HQ, Hu DH, Wang RH, Wei RP & Yan S (2015b) Assessing 62 Chinese fir (Cunninghamia lanceolata) breeding parents in a 12-year grafted clone test. Forests 6: 3799–3808. doi:10.3390/f6103799.
• Zheng HQ, Duan HJ, Hu DH, Li Y & Hao YB (2015c) Genotypic variation of Cunninghamia lanceolata revealed by phenotypic traits and SRAP markers. Dendrobiology 74: 85–94. doi:10.12657/denbio.074.009.

Identyfikatory

DOI

10.12657/denbio.079.010